The article describes the research progress of genes related with important agronomic characters in pepper (Capsicum spp.), including pungency, color, disease resistance and male sterility. The classical approaches, and new technologies associated with nextgeneration sequencing for gene isolation and cloning are presented. Deficiencies and limitations of the present study are pointed out, and the prospect for future research in accompaniment with the completeness of the pepper genomic sequencing project is discussed.